| Cell line (Human) |
K562 CRISPRi (BFP) |
This paper |
N/A |
Stable cell line with SFFV Zim3-dCas9 P2A BFP |
| Cell line (Human) |
K562 CRISPRi (GFP) |
This paper |
N/A |
Stable cell line with SFFV Zim3-dCas9 P2A GFP |
| Cell line (Human) |
K562 CRISPRi (no fluorescent marker) |
This paper |
N/A |
Stable cell line with SFFV Zim3-dCas9 P2A Hygro |
| Cell line (Human) |
RPE1 CRISPRi (Zim3) |
Replogle et al., 2022
|
N/A |
Stable cell line with SFFV Zim3-dCas9 P2A BFP |
| Cell line (Human) |
Jurkat CRISPRi (Zim3) |
This paper |
N/A |
Stable cell line with EF1alpha Zim3-dCas9 P2A mCherry |
| Cell line (Human) |
HepG2 CRISPRi |
This paper |
N/A |
Stable cell line with EF1alpha Zim3-dCas9 P2A mCherry |
| Cell line (Human) |
HT29 CRISPRi |
This paper |
N/A |
Stable cell line with EF1alpha Zim3-dCas9 P2A mCherry |
| Cell line (Human) |
HuTu-80 CRISPRi |
This paper |
N/A |
Stable cell line with EF1alpha Zim3-dCas9 P2A mCherry |
| Antibody |
Anti-human CD55 (clone JS11, mouse monoclonal), APC |
BioLegend |
Cat#: 311311; RRID:AB_2075857
|
Flow cytometry; 1:100 in PBS with 5% (v/v) FBS |
| Antibody |
Anti-human CD81 (clone 5A6, mouse monoclonal), APC |
BioLegend |
Cat#: 349509; RRID:AB_2564020
|
Flow cytometry; 1:100 in PBS with 5% (v/v) FBS |
| Antibody |
Anti-human CD151 (clone 50–6, mouse monoclonal), APC |
BioLegend |
Cat#: 350405; RRID:AB_10661726
|
Flow cytometry; 1:100 in PBS with 5% (v/v) FBS |
| Antibody |
Anti-human CD29 (clone TS2/16, mouse monoclonal), APC |
BioLegend |
Cat#: 303007; RRID:AB_314323
|
Flow cytometry; 1:100 in PBS with 5% (v/v) FBS |
| Antibody |
Anti-human B2M (clone 2M2, mouse monoclonal), APC |
BioLegend |
Cat#: 316312; RRID:AB_10641281
|
Flow cytometry; 1:100 in PBS with 5% (v/v) FBS |
| Antibody |
Mouse IgG1, κ Isotype Ctrl (clone MOPC-21, mouse monoclonal), APC |
BioLegend |
Cat#: 981806 |
Flow cytometry; 1:100 in PBS with 5% (v/v) FBS |
| Recombinant DNA reagent |
Plasmid pJB120_pHR-UCOE-SFFV-EGFP |
This paper |
Addgene: 188900 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pJB074_pHR-UCOE-SFFV-dCas9-HA-2xNLS-P2A-EGFP |
This paper |
Addgene: 188898 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pJB069_pHR-UCOE-SFFV-Zim3-NLS-dCas9-HA-2xNLS-P2A-EGFP |
This paper |
Addgene: 188899 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pCL63_pHR-UCOE-SFFV-SID4x-dCas9-HA-2xNLS-XTEN80-KRAB(Kox1)-P2A-EGFP |
This paper |
Addgene: 188901 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pCL51_pHR-UCOE-SFFV-dCas9-NLS-KRAB(Kox1)-MeCP2-P2A-EGFP |
This paper |
Addgene: 188902 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pCL35_pHR-UCOE-SFFV-dCas9-HA-2xNLS-XTEN80-KRAB(Kox1)-P2A-EGFP |
This paper |
Addgene: 188765 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pAG389_pHR-UCOE-SFFV-Zim3-NLS-dCas9-HA-2xNLS-P2A-Hygro |
This paper |
Addgene: 188768 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pNM1130_pHR-UCOE-EF1a-Zim3-NLS-dCas9-HA-2xNLS-loxP-P2A-EGFP-loxP |
This paper |
Addgene: 188773 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pNM1129_pHR-UCOE-SFFV-Zim3-NLS-dCas9-HA-2xNLS-loxP-P2A-EGFP-loxP |
This paper |
Addgene: 188774 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pNM1128_pHR-UCOE-EF1a-Zim3-NLS-dCas9-HA-2xNLS-mTagBFP2 |
This paper |
Addgene:188775 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pNM1127_pHR-UCOE-SFFV-Zim3-NLS-dCas9-HA-2xNLS-mTagBFP2 |
This paper |
Addgene: 188776 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pNM1125_pHR-UCOE-EF1a-Zim3-NLS-dCas9-HA-2xNLS-P2A-mTagBFP2 |
This paper |
Addgene:188777 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pNM1124_pHR-UCOE-EF1a-Zim3-NLS-dCas9-HA-2xNLS-P2A-EGFP |
This paper |
Addgene: 188778 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pNM1123_pHR-UCOE-SFFV-Zim3-NLS-dCas9-HA-2xNLS-P2A-mCherry |
This paper |
Addgene: 188779 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pJB109_pHR-UCOE-EF1a-Zim3-NLS-dCas9-HA-2xNLS-P2A-mCherry |
This paper |
Addgene: 188766 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pJB108_pHR-UCOE-SFFV-Zim3-NLS-dCas9-HA-2xNLS-P2A-mTagBFP2 |
This paper |
Addgene: 188767 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pRAP0006_pHR-UCOE-EF1a-dCas9-HA-2xNLS-XTEN80-KRAB(Kox1)-IRES-mCherry |
This paper |
Addgene: 188769 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pRAP0003_pHR-UCOE-SFFV-dCas9-HA-2xNLS-XTEN80-KRAB(Kox1)-IRES-mCherry |
This paper |
Addgene: 188770 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pCL75_pHR-UCOE-EFS-dCas9-HA-2xNLS-XTEN80-KRAB(Kox1)-P2A-EGFP |
This paper |
Addgene: 188771 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pCL74_pHR-UCOE-CMV-dCas9-HA-2xNLS-XTEN80-KRAB(Kox1)-P2A-EGFP |
This paper |
Addgene: 188772 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
Plasmid pCRISPRia-v2 (parent vector) |
DOI: 10.7554/eLife.19760 |
Addgene: 84832 |
|
| Recombinant DNA reagent |
Plasmid pU6-sgRNA EF1alpha-puro-T2A-mCherry |
This paper |
Addgene: 188780 |
Further information in Supplementary file 7
|
| Recombinant DNA reagent |
pJR98 |
This paper |
Addgene: 187239 |
CR3 constant region – hU6 sgRNA promoter flanked by BsmBI sites. Further information in Supplementary file 7
|
| Recombinant DNA reagent |
pJR100 |
This paper |
Addgene: 187240 |
Lentiviral sgRNA vector for Perturb-seq with mU6 sgRNA promoter, CR1 constant region with CS1 capture sequence in stem loop, and UCOE EF1alpha driving PURO-BFP marker expression. Further information in Supplementary file 7
|
| Recombinant DNA reagent |
pJR101 |
DOI: 10.1016/j.cell.2022.05.013/this paper |
Addgene: 187241 |
Lentiviral sgRNA vector for Perturb-seq with mU6 sgRNA promoter, CR1 constant region with CS1 capture sequence in stem loop, and UCOE EF1alpha driving PURO-GFP marker expression. Further information in Supplementary file 7
|
| Recombinant DNA reagent |
pJR103 |
This paper |
Addgene: 187242 |
Lentiviral sgRNA vector with mU6 sgRNA promoter, CR1 constant region, and UCOE EF1alpha driving PURO-BFP marker expression. Further information in Supplementary file 7
|
| Recombinant DNA reagent |
pJR104 |
This paper |
Addgene: 187243 |
Lentiviral sgRNA vector with mU6 sgRNA promoter, CR1 constant region, and UCOE EF1alpha driving PURO-GFP marker expression. Further information in Supplementary file 7
|
| Recombinant DNA reagent |
pJR106 |
This paper |
Addgene: 187244 |
Lentiviral sgRNA vector for CROP-seq with mU6 sgRNA promoter, CR1 constant region, and UCOE EF1alpha driving PURO-BFP marker expression. Further information in Supplementary file 7
|
| Recombinant DNA reagent |
pJR107 |
This paper |
Addgene: 187245 |
Lentiviral sgRNA vector for CROP-seq with mU6 sgRNA promoter, CR1 constant region, and UCOE EF1alpha driving PURO-GFP marker expression. Further information in Supplementary file 7
|
| Commercial assay or kit |
Direct-zol RNA Miniprep |
Zymo Research |
Cat#: R2051 |
|
| Commercial assay or kit |
Qubit RNA Broad Range (BR) Kit |
Thermo Fisher Scientific |
Cat#: Q10211
|
|
| Commercial assay or kit |
NucleoSpin Blood kit (XL or L) |
Macherey-Nagel |
Cat#: 740950 (XL) or 740954 (L) |
Purification of genomic DNA from cell pellets |
| Commercial assay or kit |
NEBNext Ultra II Q5 PCR MasterMix |
NEB |
Cat#: M0544 |
PCR amplification of dual-sgRNA elements from genomic DNA |
| Other |
TransIT-LT1 Transfection Reagent |
Mirus Bio |
Cat#: MIR 2300 |
Transfection reagent for lentivirus production |
| Software, algorithm |
Python scripts to count dual-sgRNA elements in sequencing data and remove recombined elements |
This paper |
N/A |
https://github.com/josephreplogle/CRISPRi-dual-sgRNA-screens, Replogle, 2022
|
| Sequence-based reagent |
Sequences of individual sgRNAs to target benchmarking genes |
This paper |
N/A |
Sequences listed in Supplementary file 8
|
| Sequence-based reagent |
Library dJR004, Pilot genome-wide single-sgRNA human CRISPRi library |
This paper |
N/A |
sgRNA targeting sequences in Supplementary file 1
|
| Sequence-based reagent |
Library dJR020, Pilot genome-wide dual-sgRNA human CRISRi library |
This paper |
N/A |
sgRNA targeting sequences in Supplementary file 1
|
| Sequence-based reagent |
Library dJR072, Final genome-wide, sgRNA 1+2, dual-sgRNA human CRISPRi library with UMIs |
This paper |
Addgene: 187246 |
sgRNA targeting sequences in Supplementary file 4
|
| Sequence-based reagent |
Library dJR073, Final genome-wide, sgRNA 3+4, dual-sgRNA human CRISPRi library with UMIs |
This paper |
Addgene: 187247 |
sgRNA targeting sequences in Supplementary file 4
|
| Sequence-based reagent |
Library dJR074, Final genome-wide, sgRNA 5+6, dual-sgRNA human CRISPRi library with UMIs |
This paper |
Addgene: 187248 |
sgRNA targeting sequences in Supplementary file 4
|
| Sequence-based reagent |
Library dJR075, Final genome-wide, sgRNA 1+2, dual-sgRNA human CRISPRa library with UMIs |
This paper |
Addgene: 187249 |
sgRNA targeting sequences in Supplementary file 9
|
| Sequence-based reagent |
Library dJR076, Final genome-wide, sgRNA 3+4, dual-sgRNA human CRISPRa library with UMIs |
This paper |
Addgene: 187250 |
sgRNA targeting sequences in Supplementary file 9
|
| Sequence-based reagent |
Library dJR077, Final genome-wide, sgRNA 5+6, dual-sgRNA human CRISPRa library with UMIs |
This paper |
Addgene: 187251 |
sgRNA targeting sequences in Supplementary file 9
|
